Trainable Segmentation library refactorization

[Ignacio Arganda-Carreras]

Dear Trainable Segmentation users and developers,

The original Trainable Segmentation library and plugins (Trainable Segmentation and Advanced Weka Segmentation) have been refactored for the sake of simplicity into a unified plugin and library called Trainable Weka Segmentation.

The plugin is just a renaming of the former Advanced Weka Segmentation so it keeps complete back-compatibility. The old and unmaintained Trainable Segmentation plugin has been marked as deprecated and moved to Plugins > Segmentation > deprecated.

Please, let me know if you find any problem with the new structure of the library.

Best regards,

ignacio

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: (001) 617-324-3747
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

[Gabriel Landini]

Under linux, the updater/installer fails to download the "glow (OU).lut" file.

I guess that this is related to an annoying space in the file name.
What about using and underscore instead?

Cheers

Gabriel

[Curtis Rueden]

Hi Gabriel,

> the updater/installer fails to download the "glow (OU).lut" file.

Thanks for the bug report. Yes, apparently there is a bug in the updater now when files contain spaces. I verified by looking at the structure of the fiji.sc update site and noticing that the newly updated file was called simply "glow" without the necessary extension and timestamp suffix. To fix and avoid the issue, I tweaked the metadata on the update site.

I also filed a ticket for the problem in general:

http://trac.imagej.net/ticket/1867

Regards,

Curtis

P.S. The reason I included that "annoying" space is because LUTs appear in the menu structure verbatim, so if you want it to be labeled a certain way the file name must match.

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[Wayne Rasband]

On May 14, 2013, at 12:12 PM, Curtis Rueden wrote:

> Hi Gabriel,
>
> > the updater/installer fails to download the "glow (OU).lut" file.
>
> Thanks for the bug report. Yes, apparently there is a bug in the updater now when files contain spaces. I verified by looking at the structure of the fiji.sc update site and noticing that the newly updated file was called simply "glow" without the necessary extension and timestamp suffix. To fix and avoid the issue, I tweaked the metadata on the update site.
>
> I also filed a ticket for the problem in general:
> http://trac.imagej.net/ticket/1867
>
> Regards,
> Curtis
>
> P.S. The reason I included that "annoying" space is because LUTs appear in the menu structure verbatim, so if you want it to be labeled a certain way the file name must match.

Starting with the v1.47r daily build, ImageJ replaces underscores with spaces when adding LUTs to the Image>Lookup Tables menu.

-wayne

[Curtis Rueden]

Hi Wayne,

> Starting with the v1.47r daily build, ImageJ replaces underscores with

> spaces when adding LUTs to the Image>Lookup Tables menu.

I really appreciate the thought, but isn't it too late now? Fiji already ships with some other LUTs that contain underscores in the name, such as "blue_orange_icb". Won't this change cause problems with existing macros?

E.g.:

   run("blue_orange_icb");

would become:

   run("blue orange icb");

I suppose you could support both internally, or still record and expect the version with underscores. However, I tested with today's daily build and encountered the following behavior:

- Running "blue orange icb" directly out of the menu pops an error dialog with "Unrecognized command: blue orange icb".

- Running the following macro has the same issue: run("blue orange icb");

- But running the following macro works as before: run("blue_orange_icb");

Regards,

Curtis

[Wayne Rasband]

Hi Curtis,

On May 15, 2013, at 1:33 PM, Curtis Rueden wrote:

> Hi Wayne,
>
> > Starting with the v1.47r daily build, ImageJ replaces underscores with
> > spaces when adding LUTs to the Image>Lookup Tables menu.
>
> I really appreciate the thought, but isn't it too late now? Fiji already ships with some other LUTs that contain underscores in the name, such as "blue_orange_icb". Won't this change cause problems with existing macros?
>
> E.g.:
> run("blue_orange_icb");
> would become:
> run("blue orange icb");

This is not a problem in ImageJ because it looks for "blue orange icb.lut" if it does not find "blue_orange_icb.lut". It is a problem in Fiji because it uses different code to load LUTs. ImageJ could work around the problem by not converting underscores to spaces when running in the Fiji environment. Is the best way to check for Fiji to look for "Fiji" in the title of the main window?

Best regards,

-wayne

[Johannes Schindelin]

Dear Wayne,

On Wed, 15 May 2013, Wayne Rasband wrote:

> Is the best way to check for Fiji to look for "Fiji" in the title of
> the main window?

It is a bad idea to check for the title of the main window, in particular
because it only works when you restrict yourself to a single-user,
single-machine, single-desktop, single-everything, interactive
environment.

But as you know, Fiji supports more than just that.

The best idea would be to make it unnecessary for Fiji to special-case
anything. Unfortunately, there have been a couple of instances where Fiji
introduced new features that were then imitated by ij.jar in an
incompatible way, forcing me to keep the work-arounds alive, and I fear
that this here is probably exactly such a case.

Ciao,
Johannes